The classification of species-rich genera is one of the most challenging tasks in systematics. In this paper we present an updated infrageneric classification of the genus Peperomia (Piperaceae), one of the most species-rich genera of plants. The classification is based on a molecular phylogeny of 190 accessions and the placement of 1340 of the 1606 currently accepted taxa within this classification. We provide the most comprehensive circumscriptions of Peperomia subgenera since the work of Dahlstedt in 1900, with five newly described subgenera. Fourteen monophyletic groups were revealed by phylogenetic reconstructions, including two newly discovered clades. Extensive field work, monitoring of representative living collections in our botanical gardens, and herbarium studies were the basis for morphological assignment of 80% of Peperomia species to the subgenera recognized and described herein. This work, in combination with the detailed descriptions of these subgenera, will aid field botanists, taxonomists, and ecologists to properly collect and identify species. Although parallel evolution of characters makes identification of species within Peperomia difficult, especially in species-rich clades, the key to subgenera will provide a useful framework for anyone interested in this genus and will be a reference for further studies in Peperomia.